 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 17, 2018 |
| Title |
LCMV-OVA_Spleen_d3_1 |
| Sample type |
SRA |
| |
|
| Source name |
adoptively transfered OT-1
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
pathogen: LCMV-OVA
day post infection: 3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Splenic and CNS-infiltrating OT-1 cells were FACS sorted with Aria II and RNA was harvested using Trizol reagent.
RNA-samples were prepared with the "TruSeq RNA Sample Prep Kit v2" according to the manufacturer's protocol (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequence images were transformed to BCL files with the Illumina BaseCaller software and samples were demultiplexed to FASTQ files with CASAVA (version 1.8.2).
Sequences were aligned to the genome reference sequence of Mus Musculus (UCSC genome assembly version mm10). Alignment was performed using the STAR alignment software (Dobin et al., 2012; version 2.3.0e) allowing for 2 mismatches within 50 bases.
Conversion of resulting SAM files to sorted BAM files, filtering of unique hits and counting was conducted with SAMtools (Li et al., 2009, version 0.1.18) and HTSeq (Anders et al., 2014, version 0.6.1p1).
Data was preprocessed and analyzed in the R/Bioconductor environment (www.bioconductor.org) using the DESeq2 package (Love et al., 2014, version 1.8).
Candidate genes were filtered to a minimum of 2-fold change and FDR-corrected p-value < 0.05. Gene annotation was performed using Mus musculus entries from Ensembl (www.ensembl.org) via the biomaRt package (Durinck et al., 2005, version 2.18.0).
Genome_build: mm10 (UCSC)
Supplementary_files_format_and_content: tab-delimited count files as obtained from HTSeq
|
| |
|
| Submission date |
Jan 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Gabriela Salinas |
| E-mail(s) |
[email protected]
|
| Organization name |
Universitaetsmedizin Goettingen
|
| Department |
Department of Pathology
|
| Lab |
NGS Integrative Genomics
|
| Street address |
Kreuzbergring 57
|
| City |
Goettingen |
| State/province |
Lower-Saxony |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE93805 |
Next Generation Sequencing of splenic- and CNS-infiltrating OT-1 cells in ODC-OVA mice upon LCMV-OVA and Lm-OVA infection |
|
| Relations |
| BioSample |
SAMN06239542 |
| SRA |
SRX2501600 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2462717_Sample_r697sLCMV1OVASpleen3_mm_rna_sr_Merkler_A_1_geneCounts.txt.gz |
139.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
